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Old 09-19-2011, 07:49 AM   #1
Location: EU

Join Date: Sep 2010
Posts: 52
Default Bowtie Illumina paired end reads alignment

Hello all,

I am new to NGS and trying to align illumina paired end data to a region which is of approximately 100kb where as the sequenced genome is about 1gb. Here i wanted to identify single pairs mapped to end of this region where as its other pair doesnot. How could i achieve this easily? Which is better bowtie or BWA? i used following command in bowtie but not working properly.

 bowtie -t -a -m 5 -S -p 10 -X 600 -1 001.fastq -2 002.fastq --al aligned_out
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